|
| Status |
Public on Dec 28, 2018 |
| Title |
3D Collagen 1 |
| Sample type |
SRA |
| |
|
| Source name |
murine oviductal epithelial (MOE) cell line
|
| Organism |
Mus musculus |
| Characteristics |
treatment: 3D Collagen
mouse strain: FVB
cell type: murine oviductal epithelial cells
|
| Treatment protocol |
MOE Cells were plated on 2D or 3D collagen gels for 6 hours in standard MOE media without EGF.
|
| Growth protocol |
At confluence cells were collected with trypsin and plated on 2D or 3D collagen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with TRIzol and purified with a Qiagen Rnease kit per the manufacter's intructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
3D-1
|
| Data processing |
Reads were aligned to mm10 using STARversion 020201 and default parameters
Gene counting was performed using htseq-count version 0.6.1p1 and default parameters
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts (by DESeq2) for each Sample
|
| |
|
| Submission date |
Mar 27, 2018 |
| Last update date |
Dec 28, 2018 |
| Contact name |
Joanna Burdette |
| E-mail(s) |
joannab@uic.edu
|
| Phone |
312-996-6153
|
| Organization name |
University of Illinois at Chicago
|
| Street address |
900 S. Ashland Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60607 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE112397 |
Colonization of the Ovary and Metastasis of Fallopian Tube Derived Cancer |
|
| Relations |
| BioSample |
SAMN08801734 |
| SRA |
SRX3853489 |
